Already many very nice train routes mentioned here.

I would like to add four of my favourites in Germany plus a route in France and the Netherlands:
- Dresden to Prague (Elbtalbahn - nice route along the "Elbe Gorge" with beautiful cities at both ends of the line)
- Wetzlar - Koblenz (Lahntalbahn - connecting with the trains along the Rhine)
- Stade - Cuxhaven - Bremerhaven (Niederelbebahn - if you want to see some north sea and flat land ...)
- Kiel - Husum - St. Peter Ording (Eiderstedtquerbahn - via Jübeck and Rendsburg - a nice rural route)
- Montpellier to Nice (nice Provencal landscape with many stopover-oppotunities ...)
- Utrecht - Groningen (if you travel around the tulip blooming season)